{"action":"created","issue":{"url":"https://api.github.com/repos/nimble-dev/nimble/issues/429","repository_url":"https://api.github.com/repos/nimble-dev/nimble","labels_url":"https://api.github.com/repos/nimble-dev/nimble/issues/429/labels{/name}","comments_url":"https://api.github.com/repos/nimble-dev/nimble/issues/429/comments","events_url":"https://api.github.com/repos/nimble-dev/nimble/issues/429/events","html_url":"https://github.com/nimble-dev/nimble/issues/429","id":234656388,"number":429,"title":"Linux build failure as of 7a0c518","user":{"login":"fritzo","id":648532,"avatar_url":"https://avatars3.githubusercontent.com/u/648532?v=3","gravatar_id":"","url":"https://api.github.com/users/fritzo","html_url":"https://github.com/fritzo","followers_url":"https://api.github.com/users/fritzo/followers","following_url":"https://api.github.com/users/fritzo/following{/other_user}","gists_url":"https://api.github.com/users/fritzo/gists{/gist_id}","starred_url":"https://api.github.com/users/fritzo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fritzo/subscriptions","organizations_url":"https://api.github.com/users/fritzo/orgs","repos_url":"https://api.github.com/users/fritzo/repos","events_url":"https://api.github.com/users/fritzo/events{/privacy}","received_events_url":"https://api.github.com/users/fritzo/received_events","type":"User","site_admin":false},"labels":[{"id":106487466,"url":"https://api.github.com/repos/nimble-dev/nimble/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2017-06-08T21:06:27Z","updated_at":"2017-06-20T18:44:18Z","closed_at":null,"body":"The commit 7a0c518 breaks my linux build, and I can no longer install Nimble. This is a rather large commit, and it's difficult to pinpoint the error.\r\n```\r\n$ git checkout 7a0c518  # A.k.a. devel at the momement.\r\n$ R CMD build\r\n...\r\n$ R CMD INSTALL nimble_0.6-6.tar.gz\r\n* installing to library ‘/home/fritz/R/x86_64-pc-linux-gnu-library/3.4’\r\n* installing *source* package ‘nimble’ ...\r\nchecking for g++... g++\r\nchecking whether the C++ compiler works... yes\r\nchecking for C++ compiler default output file name... a.out\r\nchecking for suffix of executables... \r\nchecking whether we are cross compiling... no\r\nchecking for suffix of object files... o\r\nchecking whether we are using the GNU C++ compiler... yes\r\nchecking whether g++ accepts -g... yes\r\nworking on eigen\r\nchecking how to run the C++ preprocessor... clang++ -Qunused-arguments -E\r\nchecking for grep that handles long lines and -e... /bin/grep\r\nchecking for egrep... /bin/grep -E\r\nchecking for ANSI C header files... yes\r\nchecking for sys/types.h... yes\r\nchecking for sys/stat.h... yes\r\nchecking for stdlib.h... yes\r\nchecking for string.h... yes\r\nchecking for memory.h... yes\r\nchecking for strings.h... yes\r\nchecking for inttypes.h... yes\r\nchecking for stdint.h... yes\r\nchecking for unistd.h... yes\r\nchecking Eigen/Dense usability... no\r\nchecking Eigen/Dense presence... no\r\nchecking for Eigen/Dense... no\r\nUsing the version of Eigen provided with NIMBLE\r\nUsing CppAD directory \r\nNIMBLE_DIR = /home/fritz/R/x86_64-pc-linux-gnu-library/3.4/nimble\r\nENABLE_LIB=true\r\nconfigure: creating ./config.status\r\nconfig.status: creating inst/make/Makevars\r\nconfig.status: creating inst/make/Makevars_lib\r\nconfig.status: creating R/config.R\r\nconfig.status: creating src/Makevars\r\nBuilding libnimble\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppUtils.cpp -o RcppUtils.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c EigenTypedefs.cpp -o EigenTypedefs.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c eigenUsingClasses.cpp -o eigenUsingClasses.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppNimbleUtils.cpp -o RcppNimbleUtils.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Utils.cpp -o Utils.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c NamedObjects.cpp -o NamedObjects.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ModelClassUtils.cpp -o ModelClassUtils.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c accessorClasses.cpp -o accessorClasses.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dists.cpp -o dists.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nimDists.cpp -o nimDists.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dllFinalizer.cpp -o dllFinalizer.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nimbleGraph.cpp -o nimbleGraph.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c smartPtrs.cpp -o smartPtrs.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c predefinedNimbleLists.cpp -o predefinedNimbleLists.o\r\ng++  -I/usr/share/R/include -DNDEBUG -I\"../include\"     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nimOptim.cpp -o nimOptim.o\r\nlinking libnimble.so\r\nLinux   \r\ng++  -shared -o libnimble.so  RcppUtils.o EigenTypedefs.o eigenUsingClasses.o RcppNimbleUtils.o Utils.o NamedObjects.o ModelClassUtils.o accessorClasses.o dists.o nimDists.o dllFinalizer.o nimbleGraph.o smartPtrs.o predefinedNimbleLists.o nimOptim.o \r\nrm *.o\r\n** libs\r\nclang++ -Qunused-arguments -I/usr/share/R/include -DNDEBUG -I../inst/include  -I     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nimble.cpp -o nimble.o\r\nclang++ -Qunused-arguments -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o nimble.so nimble.o -L../inst/CppCode -lnimble -Wl,-rpath=/home/fritz/R/x86_64-pc-linux-gnu-library/3.4/nimble/CppCode -llapack -lblas -L/usr/lib/R/lib -lR\r\n/usr/bin/ld: nimble.o: relocation R_X86_64_32 against `CallEntries' can not be used when making a shared object; recompile with -fPIC\r\nnimble.o: error adding symbols: Bad value\r\nclang: error: linker command failed with exit code 1 (use -v to see invocation)\r\n/usr/share/R/share/make/shlib.mk:6: recipe for target 'nimble.so' failed\r\nmake: *** [nimble.so] Error 1\r\nmake: Target 'all' not remade because of errors.\r\nERROR: compilation failed for package ‘nimble’\r\n* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/3.4/nimble’\r\n* restoring previous ‘/home/fritz/R/x86_64-pc-linux-gnu-library/3.4/nimble’\r\n```"},"comment":{"url":"https://api.github.com/repos/nimble-dev/nimble/issues/comments/309851505","html_url":"https://github.com/nimble-dev/nimble/issues/429#issuecomment-309851505","issue_url":"https://api.github.com/repos/nimble-dev/nimble/issues/429","id":309851505,"user":{"login":"paciorek","id":2501598,"avatar_url":"https://avatars1.githubusercontent.com/u/2501598?v=3","gravatar_id":"","url":"https://api.github.com/users/paciorek","html_url":"https://github.com/paciorek","followers_url":"https://api.github.com/users/paciorek/followers","following_url":"https://api.github.com/users/paciorek/following{/other_user}","gists_url":"https://api.github.com/users/paciorek/gists{/gist_id}","starred_url":"https://api.github.com/users/paciorek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paciorek/subscriptions","organizations_url":"https://api.github.com/users/paciorek/orgs","repos_url":"https://api.github.com/users/paciorek/repos","events_url":"https://api.github.com/users/paciorek/events{/privacy}","received_events_url":"https://api.github.com/users/paciorek/received_events","type":"User","site_admin":false},"created_at":"2017-06-20T18:44:18Z","updated_at":"2017-06-20T18:44:18Z","body":"just a note that my Ubuntu machine is using -fpic (this is with g++) and I'm not having any problems."}}
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